Fast5Summary-class: An S4 class for summarised data from a MinION sequencing run

In IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data

Description

An S4 class for summarised data from a MinION sequencing run

Usage

## S4 method for signature 'Fast5Summary'
length(x)

## S4 method for signature 'Fast5Summary'
readInfo(x)

## S4 method for signature 'Fast5Summary'
eventData(x)

## S4 method for signature 'Fast5Summary'
baseCalled(x)

## S4 method for signature 'Fast5Summary'
fastq(x)

## S4 method for signature 'Fast5Summary,ANY,ANY,ANY'
x[i]

## S4 method for signature 'Fast5Summary'
fastqTemplate(x)

## S4 method for signature 'Fast5Summary'
fastqComplement(x)

## S4 method for signature 'Fast5Summary'
fastq2D(x)

Arguments

x	Object of class Fast5Summary
i	Vector defining index to subset by.

Value

An object of class Fast5Summary

Methods (by generic)

• length: Returns the number of files read during creation of the object

• readInfo: Returns readInfo data.frame

• eventData: Returns eventData data.frame

• baseCalled: Returns baseCalled data.frame

• fastq: Returns ShortReadQ object stored in fastq slot.

• [: Subset object and return an object of the same class.

• fastqTemplate: Returns ShortReadQ object containing only template reads

• fastqComplement: Returns ShortReadQ object containing only complement reads

• fastq2D: Returns ShortReadQ object containing only 2D reads

Slots

readInfo

Object of class tibble. Contains five columns:

• id - an integer key that allows use to match entries in the separate slots of this object.

• file - Basename of the fast5 file the data was read from.

• read - Read number from channel.

• channel - channel.

• mux - Specific pore that was used within the four that are assigned to a single channel. Should be in the range 1-4, but if this isn't available it will be 0.

rawData

Object of class tibble. Intended to hold raw signal data although reading this is currently not implemented in IONiseR.

eventData

Object of class tibble. Holds summary of events data prior to base calling. Contains five columns:

• id - an integer key that allows use to match entries in the separate slots of this object.

• start_time - time in seconds after the run started that this reading began.

• duration - time in seconds the reading lasted.

• num_events - the number of events that were recorded as part of this reading.

• median_signal - median of the recorded signals for this set of events.

baseCalled

Object of class tibble. For the most part contains similar data to the @eventData slot, the base called data is derived from it.

• id - an integer key that allows use to match entries in the separate slots of this object.

• start_time - time in seconds after the run started that this reading began.

• duration - time in seconds the reading lasted.

• num_events - the number of events that were recorded as part of this reading.

• strand - can be either 'template' or 'complement'

• full_2D - boolean value specifying whether the read forms part of a 2D pair. If TRUE the FASTQ data for the template, complement and 2D read will be available in the @fastq slot.

fastq

Object of class ShortReadQ. This slot contains all reads (template, complement and 2D). The read names take the form NUM_STRAND, where NUM matches with the id column in the other slots and STRAND indicates whether the read is template, complement or 2D.

versions

A list intended to store the version of IONiseR that was used to create the object. (May be extended in the future to include the version of MinKNOW that the original fast5 files were processed, if this can be determined accurately.)

Examples

if( require(minionSummaryData) ) {
   data(s.typhi.rep2, package = 'minionSummaryData')
   length( s.typhi.rep2 )
}

IONiseR documentation built on Nov. 8, 2020, 6 p.m.